3HQP

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PKLPDB ENTRY 1PKL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.227710-16% PEG8000, 20mM triethanolamine-HCl, 50mM MgCl2, 100mM KCl, 10-15% glycerol, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3162.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.486α = 89.73
b = 151.14β = 80.17
c = 160.319γ = 71.64
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2008-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.98ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.341.9694.70.0958.21.99138764701142.32.341.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4290.80.6381.31.365953

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PKL2.334.464462602357994.630.201110.198410.25198RANDOM42.789
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-2.770.290.16-0.41-0.842.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.789
r_dihedral_angle_4_deg16.527
r_dihedral_angle_3_deg16.234
r_dihedral_angle_1_deg4.96
r_scangle_it1.391
r_angle_refined_deg1.106
r_scbond_it0.87
r_mcangle_it0.492
r_nbtor_refined0.294
r_mcbond_it0.254
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.789
r_dihedral_angle_4_deg16.527
r_dihedral_angle_3_deg16.234
r_dihedral_angle_1_deg4.96
r_scangle_it1.391
r_angle_refined_deg1.106
r_scbond_it0.87
r_mcangle_it0.492
r_nbtor_refined0.294
r_mcbond_it0.254
r_metal_ion_refined0.21
r_symmetry_vdw_refined0.188
r_nbd_refined0.182
r_symmetry_hbond_refined0.14
r_xyhbond_nbd_refined0.135
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms60784
Nucleic Acid Atoms
Solvent Atoms4100
Heterogen Atoms973

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
SCALAdata scaling